Package: YAPSA
Type: Package
Title: Yet Another Package for Signature Analysis
Version: 1.37.0
Date: 2025-07-22
Authors@R: c(person("Daniel", "Huebschmann", role = "aut"),
    person("Lea", "Jopp-Saile", role = "aut"),
    person("Carolin", "Andresen", role = "aut"),
    person("Zuguang", "Gu", role = c("aut", "cre"), email = "z.gu@dkfz.de"),
    person("Matthias", "Schlesner", role = "aut"))
Imports: limSolve, SomaticSignatures, VariantAnnotation, Seqinfo,
        reshape2, gridExtra, corrplot, dendextend, GetoptLong,
        circlize, gtrellis, doParallel, parallel, PMCMRplus,
        ggbeeswarm, ComplexHeatmap, KEGGREST, grDevices, Biostrings,
        BSgenome.Hsapiens.UCSC.hg19, magrittr, pracma, dplyr, utils
Depends: R (>= 4.0.0), GenomicRanges, ggplot2, grid
Description: This package provides functions and routines for
        supervised analyses of mutational signatures (i.e., the
        signatures have to be known, cf. L. Alexandrov et al., Nature
        2013 and L. Alexandrov et al., Bioaxiv 2018). In particular,
        the family of functions LCD (LCD = linear combination
        decomposition) can use optimal signature-specific cutoffs which
        takes care of different detectability of the different
        signatures. Moreover, the package provides different sets of
        mutational signatures, including the COSMIC and PCAWG SNV
        signatures and the PCAWG Indel signatures; the latter infering
        that with YAPSA, the concept of supervised analysis of
        mutational signatures is extended to Indel signatures. YAPSA
        also provides confidence intervals as computed by profile
        likelihoods and can perform signature analysis on a stratified
        mutational catalogue (SMC = stratify mutational catalogue) in
        order to analyze enrichment and depletion patterns for the
        signatures in different strata.
License: GPL-3
Suggests: testthat, BiocStyle, knitr, rmarkdown
VignetteBuilder: knitr
LazyLoad: yes
biocViews: Sequencing, DNASeq, SomaticMutation, Visualization,
        Clustering, GenomicVariation, StatisticalMethod,
        BiologicalQuestion
RoxygenNote: 7.2.3
Encoding: UTF-8
Config/pak/sysreqs: libgmp3-dev make libbz2-dev libicu-dev liblzma-dev
        libpng-dev libxml2-dev libmpfr-dev libssl-dev perl xz-utils
        zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 14:34:03 UTC
RemoteUrl: https://github.com/bioc/YAPSA
RemoteRef: HEAD
RemoteSha: f37ad09f66a3061a68b52f2aed18dd9c56e5b957
NeedsCompilation: no
Packaged: 2025-11-01 03:02:14 UTC; root
Author: Daniel Huebschmann [aut],
  Lea Jopp-Saile [aut],
  Carolin Andresen [aut],
  Zuguang Gu [aut, cre],
  Matthias Schlesner [aut]
Maintainer: Zuguang Gu <z.gu@dkfz.de>
Built: R 4.6.0; ; 2025-11-01 03:07:16 UTC; windows
